Align Alr3027 protein, component of The 2-oxo monocarboxylate transporter (Pernil et al., 2010). Transports pyruvate which is inhibited by various 2-ketoacids (characterized)
to candidate Ac3H11_155 TRAP dicarboxylate transporter, DctM subunit, unknown substrate 5
Query= TCDB::Q8YSQ7 (445 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_155 Length = 432 Score = 218 bits (554), Expect = 4e-61 Identities = 132/431 (30%), Positives = 226/431 (52%), Gaps = 21/431 (4%) Query: 26 VAFSLGGVAILFGLLGIGLGVFDPIFLTA---------------MPQRIFGIMANYTLLA 70 V +LG + +LF +LG GL + + A M I+G +++TL A Sbjct: 3 VIIALGLIVVLFAVLGSGLWIGLSLLAVALVGMELFTNRPVGDSMMLTIWGSTSSWTLTA 62 Query: 71 IPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGVVAATVVAM 130 +P F++MG +L +S ++ + + + L RL G L V+ + AA +G AAT + Sbjct: 63 LPLFLWMGEILFRSKLSSSMFKGLAPWLERLPGRLLHVNVVGCTIFAAISGSSAATCATI 122 Query: 131 GLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLGISVGDLFIGSVIPG 190 G I+LP + + GY +E++ G +A +GTLG +IPPS++++V G +S+ LF+ VIPG Sbjct: 123 GKITLPELKQRGYPEEISVGTLAGAGTLGLLIPPSIIMIVYGVAANVSISKLFLAGVIPG 182 Query: 191 LMMASAFALHVLIVAFIRPDVAPALPAQVREIGGKALGKRVIQVMIPPLILILLVLGSIF 250 L++A+ F ++++ A D PA AQ+ K R +IP + LI++VLG+I+ Sbjct: 183 LLLAALFMGYIIVWALFNKDKVPAPDAQL-SFAQKLYASR---HLIPVVSLIVVVLGAIY 238 Query: 251 FGFATPTEAGAVGCAGAIALAAANGQFTLESLRQVCDTTLRITSMVVFILIGSTAFSLVF 310 G AT TEA A+G AG++ LA G ++ R+ M+ IL G+ +L Sbjct: 239 SGIATATEAAALGVAGSLILAKIEGSLNWARFKEGLVAACRVYCMIGLILAGAAFLTLAM 298 Query: 311 RGLNGDQFMFDVLANLPGGKIGFLFVSMTTVFLLGFFIDFFEIAFIVIPLFVPVAQKLGI 370 + + + + + L + + + LLG F+D + + I + +P + G Sbjct: 299 GFIGLPRHLAEFIGALHLSPFALMLLLIVFFILLGCFLDGISMVVLTIAVLLPTVEAAGF 358 Query: 371 DLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPPEVTTSDIYRGVIPFILLQLLVLLLI 430 DLVW+G+ + ++ + +TPP GF LF L+G+ EVT I R +P L ++ +++ Sbjct: 359 DLVWFGIFIVLVVEMAQITPPVGFNLFVLQGMTRREVTW--IARTALPLFALMIVAVIMT 416 Query: 431 IIFPGIVSFLP 441 P +V +LP Sbjct: 417 YFVPDVVLWLP 427 Lambda K H 0.331 0.149 0.437 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 489 Number of extensions: 26 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 445 Length of database: 432 Length adjustment: 32 Effective length of query: 413 Effective length of database: 400 Effective search space: 165200 Effective search space used: 165200 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory